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Yorodumi- PDB-1g2z: DIMERIZATION DOMAIN OF HNF-1ALPHA WITH A LEU 13 SELENOMETHIONINE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g2z | ||||||
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Title | DIMERIZATION DOMAIN OF HNF-1ALPHA WITH A LEU 13 SELENOMETHIONINE SUBSTITUTION | ||||||
Components | HEPATOCYTE NUCLEAR FACTOR 1-ALPHA | ||||||
Keywords | TRANSCRIPTION / dimerization domain / four-helix bundle / transcription factor / selenomethionine | ||||||
Function / homology | Function and homology information paraxial mesoderm formation / cellular response to rapamycin / apoptotic nuclear changes / regulation of NADP metabolic process / renal D-glucose absorption / reproductive structure development / regulation of hormone secretion / bile acid biosynthetic process / cellular response to L-leucine / reverse cholesterol transport ...paraxial mesoderm formation / cellular response to rapamycin / apoptotic nuclear changes / regulation of NADP metabolic process / renal D-glucose absorption / reproductive structure development / regulation of hormone secretion / bile acid biosynthetic process / cellular response to L-leucine / reverse cholesterol transport / pronucleus / regulation of Wnt signaling pathway / pancreas development / negative regulation of miRNA processing / insulin secretion / bile acid and bile salt transport / embryonic limb morphogenesis / positive regulation of mitochondrial membrane potential / heme biosynthetic process / positive regulation of ATP biosynthetic process / negative regulation of peptidyl-threonine phosphorylation / D-glucose import / blastocyst development / photoreceptor outer segment / bone resorption / response to glucose / fatty acid transport / cholesterol metabolic process / liver development / transcription coregulator binding / cellular response to glucose stimulus / placenta development / positive regulation of insulin secretion / transcription coactivator binding / fatty acid biosynthetic process / protein localization / glucose homeostasis / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / response to oxidative stress / sequence-specific DNA binding / transcription by RNA polymerase II / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein dimerization activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / positive regulation of protein phosphorylation / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / regulation of DNA-templated transcription / positive regulation of gene expression / negative regulation of apoptotic process / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.15 Å | ||||||
Authors | Rose, R.B. / Endrizzi, J.A. / Cronk, J.D. / Holton, J. / Alber, T. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: High-resolution structure of the HNF-1alpha dimerization domain. Authors: Rose, R.B. / Endrizzi, J.A. / Cronk, J.D. / Holton, J. / Alber, T. #1: Journal: Nat.Struct.Biol. / Year: 2000 Title: Structural basis of dimerization, coactivator recognition and MODY3 mutations in HNF-1alpha Authors: Rose, R.B. / Bayle, J.H. / Endrizzi, J.A. / Cronk, J.D. / Crabtree, G.R. / Alber, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g2z.cif.gz | 24.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g2z.ent.gz | 17.1 KB | Display | PDB format |
PDBx/mmJSON format | 1g2z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g2z_validation.pdf.gz | 417.6 KB | Display | wwPDB validaton report |
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Full document | 1g2z_full_validation.pdf.gz | 418.5 KB | Display | |
Data in XML | 1g2z_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | 1g2z_validation.cif.gz | 8.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/1g2z ftp://data.pdbj.org/pub/pdb/validation_reports/g2/1g2z | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Two monomers are in the asymmetric unit, although not the biologically relevant dimer. The dimer of each of the monomers is generated by the two fold axis: -x+2, -y, z. |
-Components
#1: Protein/peptide | Mass: 3451.884 Da / Num. of mol.: 2 / Fragment: DIMERIZATION DOMAIN, RESIDUES 1-32 / Mutation: L13(MSE) / Source method: obtained synthetically Details: This peptide was chemically synthesized. The sequence of this peptide naturally occurs in mouse (Mus musculus), with a point mutation at position 13. References: UniProt: P22361 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.22 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, Tris-HCl, lithium sulphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 200 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.95372, 0.97957, 0.9798, 1.00 | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 28, 1999 / Details: Double crystal | |||||||||||||||
Radiation | Monochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.15→29.5 Å / Num. all: 22638 / Num. obs: 22638 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 10.3 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.2 | |||||||||||||||
Reflection shell | Resolution: 1.15→1.19 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 5.7 / Num. unique all: 2032 / % possible all: 90 | |||||||||||||||
Reflection | *PLUS Num. obs: 31540 / % possible obs: 93 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.066 | |||||||||||||||
Reflection shell | *PLUS Highest resolution: 1.05 Å / Lowest resolution: 1.11 Å / % possible obs: 82.1 % / Rmerge(I) obs: 0.398 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: wARP model Resolution: 1.15→29.5 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 563662.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Refinement carried out in tnt. Statistics reported from CNS (input file: model_stats.list).
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 97.28 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.15→29.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.15→1.19 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / Num. reflection Rfree: 1443 / % reflection Rfree: 5 % / Rfactor obs: 0.223 / Rfactor Rfree: 0.253 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 31.2 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.31 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.35 |